this game has so much potential, but I cannot conceive of a world where having your allies disabled or your turns skipped is in any way fun
True, but they're not really designed to be fun. I don't think everything can be designed to be purely about fun. A game like this needs some things to be an obstacle and a challenge. The fun/accomplishment comes from beating those obstacles. And they (usually) start appearing on the late game where it's throwing everything at you to give some challenge.
I understand where you're coming from, but a run of bad luck against one of those turn-skipping pirates or getting the wrong ally stunned can lose you the run on the spot. the only counterplay available is to hope you can get that one trinket that makes you immune, and you otherwise have no real solution or strategy to stop it
Well yeah, that is indeed true. And not only for skips and stuns, it's still overall way more luck reliant that I'd want it to be. I've been thinking of more stuff I could add to give more actual choice making and counterplay for some common big dangers. But still keeping it balanced so that players can't realistically survive everything (at least before the "end").